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CAREamics

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CAREamics

Home
Installation
Installation
Features
Guides
Guides
- Using CAREamics
  Using CAREamics
- Tutorials
  Tutorials
- CAREamics UI
  CAREamics UI
- FAQ
  FAQ
API Reference
API Reference
- Careamics
- Careamist
- Config
  Config
  - Configuration
  - N2V Configuration
  - Algorithms
    
    Algorithms
    
    CARE Algorithm Config
    
    HDN Algorithm Config
    
    Microsplit Algorithm Config
    
    N2N Algorithm Config
    
    N2V Algorithm Config
    
    PN2V Algorithm Config
    
    UNet Algorithm Config
    
    VAE Algorithm Config
    
    N2V Manipulation
    
    N2V Manipulation
    
    N2V Manipulate Config
  - Architectures
    
    Architectures
    
    Architecture Config
    
    LVAE Config
    
    UNet Config
  - Augmentations
    
    Augmentations
    
    Transform Unions
    
    XY Flip Config
    
    XY Random Rotate90 Config
  - Data
    
    Data
    
    Data Config
    
    Microsplit Data Config
    
    Normalization Config
    
    Patch Filter
    
    Patch Filter
    
    Mask Filter Config
    
    Max Filter Config
    
    Meanstd Filter Config
    
    Patch Filter Config
    
    Shannon Filter Config
    
    Patching Strategies
    
    Patching Strategies
    
    Random Patching Config
    
    Sequential Patching Config
    
    Stratified Patching Config
    
    Tiled Patching Config
    
    Whole Patching Config
  - Factories
    
    Factories
    
    Algorithm Factory
    
    CARE N2N Factory
    
    Config Discriminators
    
    Data Factory
    
    Factory Utils
    
    N2V Factory
    
    Training Factory
  - Lightning
    
    Lightning
    
    Optimizer Configs
    
    Parameters Filter
    
    Training Configuration
  - Losses
    
    Losses
    
    Loss Config
  - Noise Model
    
    Noise Model
    
    Likelihood Config
    
    Noise Model Config
    
    Serializers
  - Support
    
    Support
    
    Supported Activations
    
    Supported Algorithms
    
    Supported Architectures
    
    Supported Data
    
    Supported Filters
    
    Supported Loggers
    
    Supported Losses
    
    Supported Normalization
    
    Supported Optimizers
    
    Supported Patching
    
    Supported Pixel Manipulations
    
    Supported Struct Axis
    
    Supported Transforms
  - Utils
    
    Utils
    
    Configuration IO
    
    Random
  - Validators
    
    Validators
    
    Axes Validators
    
    Model Validators
    
    Patch Validators
- Dataset
  Dataset
  - Dataset
  - Image Region Data
  - Augmentation
    
    Augmentation
    
    Compose
    
    Transform
    
    XY Flip
    
    XY Random Rotate90
  - Factory
    
    Factory
    
    Factory
    
    Filter Bg
    
    Microsplit Factory
    
    Val Split
  - Image Stack
    
    Image Stack
    
    Czi Image Stack
    
    File Image Stack
    
    Image Stack Protocol
    
    In Memory Image Stack
    
    Zarr Image Stack
    
    Image Utils
    
    Image Utils
    
    Image Stack Utils
  - Image Stack Loader
    
    Image Stack Loader
    
    Image Stack Loader Protocol
    
    Image Stack Loaders
    
    Zarr Utils
  - Normalization
    
    Normalization
    
    Mean Std Normalization
    
    No Normalization
    
    Normalization
    
    Normalization Factory
    
    Range Normalization
    
    Running Mean Std
    
    Running Quantile
    
    Statistics
    
    Utils
  - Patch Constructor
    
    Patch Constructor
    
    Basic Patch Constructor
    
    Metadata Utils
    
    Microsplit Patch Constructors
    
    Patch Constructor
  - Patch Extractor
    
    Patch Extractor
    
    Limit File Extractor
    
    Patch Extractor
  - Patch Filter
    
    Patch Filter
    
    Filtermap Utils
    
    Mask Patch Filter
    
    Max Patch Filter
    
    Mean Std Patch Filter
    
    Patch Filter
    
    Patch Filter Factory
    
    Shannon Patch Filter
  - Patching
    
    Patching
    
    Fixed Patching
    
    Patch Specs
    
    Patching
    
    Patching Factory
    
    Random Patching
    
    Sequential Patching
    
    Stratified Patching
    
    Tiled Patching
    
    Whole Sample Patching
- Image IO
  Image IO
  - Read
    
    Read
    
    Get Func
    
    Tiff
  - Write
    
    Write
    
    Get Func
    
    Tiff
- Lightning
  Lightning
  - Grouped Index Sampler
  - Callbacks
    
    Callbacks
    
    Config Saver Callback
    
    Data Stats Callback
    
    Progress Bar Callback
    
    Stop Prediction Callback
    
    Prediction
    
    Prediction
    
    File Path Utils
    
    Image Write Strategy
    
    Prediction Writer Callback
    
    Tile Write Strategy
    
    Write Strategy
    
    Write Strategy Factory
    
    Zarr Tile Write Strategy
  - Data
    
    Data
    
    Data Module
    
    Data Module Utils
    
    Grouped Index Sampler
    
    Microsplit Data Module
  - Modules
    
    Modules
    
    CARE Module
    
    Get Module
    
    Module Utils
    
    N2V Module
    
    N2V Utils
    
    N2V Utils
    
    N2V Manipulate
    
    Pixel Manipulation
  - Prediction
    
    Prediction
    
    Convert Prediction
    
    Stitch Prediction
    
    LVAE
    
    LVAE
    
    LVAE Convert Outputs
    
    LVAE Prediction
    
    LVAE Stitch Prediction
    
    LVAE Tiling Manager
  - Utils
    
    Utils
    
    Csv Logger
    
    Load Checkpoint
- Losses
  Losses
  - N2V Losses
  - LVAE
    
    LVAE
    
    Loss Utils
    
    LVAE Loss Factory
    
    LVAE Losses
- LVAE Training
  LVAE Training
  - Calibration
  - Get Config
  - Lightning Module
  - Metrics
  - Train LVAE
  - Train Utils
  - Dataset
    
    Dataset
    
    Config
    
    Lc Dataset
    
    Ms Dataset Ref
    
    Multich Dataset
    
    Multicrop Dset
    
    Multifile Dataset
    
    Types
    
    Utils
    
    Utils
    
    Data Utils
    
    Empty Patch Fetcher
    
    Index Manager
    
    Index Switcher
- Metrics
  Metrics
  - Metrics
  - Psnr
- Model IO
  Model IO
  - Bmz IO
  - Model IO Utils
  - Bioimage
    
    Bioimage
    
    Bioimage Utils
    
    Cover Factory
    
    Model Description
- Models
  Models
  - Model Factory
  - Constraints
    
    Constraints
    
    Model Constraints
    
    Model Constraints Factory
    
    UNet Constraints
  - LVAE
    
    LVAE
    
    Layers
    
    Likelihoods
    
    LVAE
    
    Noise Models
    
    Stochastic
    
    Utils
  - Model Utils
    
    Model Utils
    
    Activation
  - UNet
    
    UNet
    
    Layers
    
    UNet
- Plotting
  Plotting
- References
  References
  - CARE
    
    CARE
    
    Citations
    
    Descriptions
  - N2N
    
    N2N
    
    Citations
    
    Descriptions
  - N2V
    
    N2V
    
    Citations
    
    Descriptions
  - PN2V
    
    PN2V
    
    Citations
    
    Descriptions
- Utils
  Utils
  - Autocorrelation
  - Context
  - Deprecation
  - Folder Versioning
  - Get Device
  - Logging
  - Ram
  - Reshape Array
  - Version

On this page

Data
Models
Logging

Home
Guides
Tutorials

Tutorials

Data

Custom format
Implementing an Image Stack

Models

Exporting to the BioImage Model Zoo

Logging

Logging with WandB and TensorBoard

Custom Data Formats

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